Fig. 3: Sharing of KoRV IS.
From: Retroviral integrations contribute to elevated host cancer rates during germline invasion
a Numbers of IS unique to one koala (either tumour-specific IS or IS in healthy tissue in a single koala) compared to those shared in PCA groups (shown in c). The single IS shared by ten koalas is located in the gene SLC29A1, an equilibrative nucleoside transporter. The three IS shared by five koalas were located 1 kb downstream of MAP4K4, in a 140 kb region between the genes CTNNBL1 and SRC, and in an intron of RCAN2. Insert shows percentages in the categories according to genomic location. Shared (other) refers to all IS shared between two or more koalas that are not in PCA groups. IS shared within the PCA groups are more likely to be in exons that those shared outside the groups. b From published RNA-seq data36, the expression of SLC29A1 in lymph nodes was found to be differentially expressed in northern koalas from Queensland (QLD) compared to koalas from South Australia (SA); this was the most significantly differentially expressed annotated gene between the two koala populations (using the Limma R package86 for differential expression analysis with false discovery rate used for multiple test correction: log fold change = 3.65, P = 1.35 × 10−5). Boxplots indicate the interquartile range (IQR) with the centre line showing the median; whiskers show 1.5 × IQR. c Sharing reflects the geographic proximity of the koalas with principle component analysis showing groups which correspond to proximity. Note: PCA analysis was carried out without prior knowledge of the geographic origin of each koala and led us to request the location data of the samples. d Provenance of the koalas shown on a map of coastal region bordering Queensland and New South Wales, Australia (~130 km north and south of Brisbane is shown). e Plot of number of shared IS versus geographical distance with pairs of koalas sharing the highest numbers of IS highlighted.
